WASHINGTON — When Jared Kushner hosted a high-profile summit meeting on federal prison reform at the White House last Friday, some in attendance noticed that the man who was ostensibly in charge of the federal prison system, Mark S. Inch, a retired Army major general, was nowhere in sight.

Only Mr. Kushner and a few others knew that Mr. Inch, a genial former military police commander appointed to oversee the Federal Bureau of Prisons and its more than 180,000 inmates just nine months ago, had two days earlier submitted his resignation as the bureau’s director to Deputy Attorney General Rod J. Rosenstein.

By the time President Trump entered the East Room, Mr. Inch had already been ordered to vacate his office and had begun packing up books and memorabilia from his 35-year military career.

Mr. Inch told Mr. Rosenstein he was tired of the administration flouting “departmental norms.” And he complained that Attorney General Jeff Sessions had largely excluded him from major staffing, budget and policy decisions, according to three people with knowledge of the situation. Mr. Inch also felt marginalized by Mr. Kushner, the president’s son-in-law and senior adviser, in drafting prison reform legislation, the officials said.

He found himself caught in an ideological turf war between Mr. Kushner and Mr. Sessions. Mr. Kushner has championed reforms to the corrections system and more lenient federal sentencing, and Mr. Sessions, a law-and-order conservative and former Alabama attorney general, has opposed significant parts of the bipartisan prison reform bill that Mr. Kushner backs, according to officials.

Mr. Kushner, with the president’s support, has been pushing prison reform legislation meant to reduce recidivism by incentivizing inmates — with the possibility of early release to halfway houses or home confinement — to take part in job training and other rehabilitation programs.

Early in the administration, Mr. Kushner and Mr. Sessions came to an agreement, according to a former administration official involved in their talks. Mr. Kushner would press ahead with prison reforms but avoid a politically divisive issue he cared even more strongly about, sentencing reform, which the attorney general and Senator Mitch McConnell, the majority leader, both adamantly oppose.

But Mr. Sessions, not Mr. Kushner, controls the prison bureau. And he has quietly worked to ensure that any reforms that might be seen as excessively lenient toward inmates are put into place only after time-consuming study, according to officials.

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The departure of Mark S. Inch creates a vacuum at a time when the Federal Bureau of Prisons is grappling with an existential crisis over workplace harassment and other issues.CreditU.S. Army

The departure of Mr. Inch, who tried to navigate a middle course, creates a vacuum at a time when the bureau is grappling with an existential crisis over issues about workplace harassment, violence, gang activity, sentencing fairness and the funding of rehabilitation programs.

“It’s disappointing,” said Jack Donson, director of case management and programs for FedCure, a nonprofit advocacy group for federal inmates. “The bureau finally gets someone from outside the culture who can, maybe, clean things out and within nine months he’s been railroaded out the door.”

But some see Mr. Inch’s exit as an opening for Mr. Trump to take a more sweeping approach that would include sentencing reform — one of the few issues that offer him a chance for the kind of big, bipartisan deal he promised during the 2016 campaign.

“The rap against General Inch is that he wasn’t a real reformer. In that sense, his departure is an opportunity,” said Kevin Ring, president of Families Against Mandatory Minimums, a Washington-based advocacy organization that is broadly supportive of Mr. Kushner’s reform efforts.

“There’s a real struggle going on now about whether or not to reform the bureau, and it was increasingly clear that he wasn’t in a position to reform that agency.”

A newcomer to the federal prison system, Mr. Inch never found his footing, according to interviews with current and former bureau employees. And he struggled to publicly explain his department’s response to complaints of sexual harassment, violence and staffing problems inside the system.

Internally he was marginalized, cut out of budgetary decisions and largely excluded from discussion of the prison reform bill backed by Mr. Kushner, which passed the House on Tuesday but faces an uphill battle in the Senate.

Two senior White House officials said Mr. Kushner made a point of inviting Mr. Inch to meetings on the proposed legislation, but Mr. Sessions and his staff often sent other officials in his place.

“The attorney general firmly stands behind the principles of prison reform,” said Sarah Isgur Flores, a spokeswoman for Mr. Sessions. “On this specific bill, we have worked closely with the team to offer suggestions that we believe will protect safety and improve rehabilitative outcomes.”

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Attorney General Jeff Sessions, a law-and-order conservative, has opposed significant parts of a bipartisan prison reform bill that Mr. Kushner backs.CreditTom Brenner/The New York Times

Mr. Inch was especially frustrated with a provision in a draft of the legislation, backed by Mr. Sessions, that scuttled the National Institute of Corrections, a clearinghouse for best practices and the training of wardens, which Mr. Sessions viewed as unnecessary. He also objected to the Kushner-backed requirement that inmates be placed in prisons within 500 miles of their homes. While he agreed with the idea of making it easier for families and friends to visit prisoners, he also believed that it would make it harder to move gang members beyond the reach of other members in their hometowns.

Mr. Inch and Mr. Sessions clashed repeatedly over personnel. For months Mr. Inch pleaded with Mr. Rosenstein to install Sara Revell, a regional prisons official, as his top deputy — and had repeatedly been told by Mr. Rosenstein that Mr. Sessions had not decided, without an explanation. He was also rebuffed on other appointments, and came to resent Mr. Sessions’s habit of dispatching junior department lawyers to deliver messages to him.

When Mr. Kushner praised Mr. Inch as a “change agent” during a tour of a federal prison in Texas this month, Mr. Inch joked to an associate that it would annoy Mr. Sessions.

Last week, a frustrated Mr. Inch called Mr. Rosenstein’s office to make one final stab at getting Ms. Revell hired.

Mr. Kushner had already come to view Mr. Inch as less a policy peer than an employee. This month, he summoned Mr. Inch and two federal wardens to the White House and demanded that they ease access to volunteer groups, including evangelical ministries and Jewish organizations, in federal prisons, according to two people familiar with the exchange.

Prison reform is an issue of particular interest to Mr. Kushner. In 2005, his father, Charles Kushner, was sentenced to two years in prison after pleading guilty to 18 counts of tax evasion, witness tampering and making illegal campaign donations. He served 14 months in a federal prison camp in Alabama and then was sent to a halfway house in New Jersey. He was released in August 2006.

But the bill favored by Mr. Kushner has been criticized by some prison reform advocates as impractical — in part because of a lack of available beds in halfway houses. The prison bureau decided last year not to renew contracts with a number of halfway house providers.

And in a May letter to the House Judiciary Committee, the N.A.A.C.P., along with more than 70 organizations, urged lawmakers to vote no on the legislation, explaining that any effort to pass prison reform without including sentencing reform would “not meaningfully improve the federal system.” The union that represents federal prison workers has also vocally opposed the bill.

At the White House meeting last Friday, Mr. Trump said he would sign the bill if lawmakers could get it to his desk. “Prison reform is an issue that unites people from across the political spectrum. It’s an amazing thing,” he said.

For now, the Bureau of Prisons will be run by its former assistant director, Hugh J. Hurwitz, a career bureau official. Mr. Sessions was taken by surprise when Mr. Inch resigned and has not begun his search for a permanent successor, according to a Justice Department official.

Glenn Thrush reported from Washington, and Danielle Ivory from New York.

A version of this article appears in print on , on Page A14 of the New York edition with the headline: Kushner and Sessions Turf War Led Federal Prisons Director to Step Down. Order Reprints | Today’s Paper | Subscribe